Fig. 2

Early lesion cell phenotype profiles. (a) Marker expression heatmap for the myeloid, astrocyte and T cell phenotypes, identified by PhenoGraph clustering on histoCAT using segmented cells (n = 4397). The heatmap displays relative expression levels based on Z-score normalized marker intensity values, and single cells are hierarchically clustered within each phenotype group. Labels at the bottom of the heatmap indicate the area of the lesion to which each phenotype localizes. (b) Violin plot representation of the data in (a). (c) t-SNE plot showing the distinct phenotype clusters. (d) t-SNE plot colored by marker intensity, confirming the separation of CD68⁺, S100B⁺ and CD3⁺ cell types. G/WMoR = gray and white matter outer rim; WMoR = white matter outer rim; iR = inner rim; WM R/C = white matter rim/center; C = center; NAWM = normal-appearing white matter